Making an Invisible Material in the Cycles render engine
If you want the object to disappear gradually I would do it with the material.  To make it disappear from top to bottom/side to side etc. (like a box covering it up as you described) I would se this node setup for it's material.



You can then animate the value on the greater than node (the one in yellow) from 1 to 0 to make the object disappear from top to bottom.  If you want left to right use the X value from the separate XYZ node.



This works because taking the X, Y, or Z component of the generated texture coordinates gives a gradient from 0 to 1 from left to right, front to back, or back to front respectively.  The output of this, sent through a greater than node to chop it off at a certain point, is used to drive a mix shader mixing the normal material (in this case the diffuse shader) with a transparent shader.  When you animate the value of the greater than node you are animating the cutoff point.